(p. 110) Look at Figure 4.7, which depicts the loss of oxygen over time and the transcriptional response of three genes. These data are the ratios of transcription for genes X, Y, and Z during the depletion of oxygen. Using the color scale from Figure 4.6 (bright, medium, dim green, black, dim, medium, or bright red), determine the color for each ratio in Figure 4.7b.

(p. 110) Were any of the genes in Figure 4.7b transcribed similarly?

(p. 118) Why would most spots be yellow at the first time point?

(p. 118) Go to http://www.yeastgenome.org and search for the gene TEF4; you will see it is involved in translation. Look at the time point labeled OD 3.7 in Figure 4.12, and find the TEF4 spot. Over the course of this experiment, was TEF4 induced or repressed? Hypothesize why TEF4’s gene regulation was part of the cell’s response to a reduction in available glucose (i.e., the only available food).

(p. 120) Why would TCA cycle genes be induced if the glucose supply is running out?

(p. 120) What mechanism could the genome use to ensure genes for enzymes in a common pathway are induced or repressed simultaneously?

(p. 121) Given rule one on page 109, what color would you see on a DNA chip when cells had their repressor gene TUP1 deleted?

(p. 121) What color spots would you expect to see on the chip when the transcription factor Yap1p is overexpressed?

(p. 121) Could the loss of a repressor or the overexpression of a transcription factor result in the repression of a particular gene?

(p. 121) What types of control spots would you like to see in this type of experiment? How could you verify that you had truly deleted or overexpressed a particular gene?